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Jeremy, Mac OS 9 will run natively on any G4 MDD with FireWire 400 ports. Models with FireWire 800 ports are OS X bootable only. You can download a copy of OS 9 for these machines via Macintosh Garden:

It may well be possible to overwrite the ROM on a dual-800 to boot OS 9, I've never tried it. It's also a really good way to brick your machine if something goes wrong. G4 MDDs with FW400 are easy to find, personally I'd recommend sticking with supported configurations.

All G4 Macs run OS 9 very well, a single 1.25GHz G4 will be quite zippy. Mac OS 9 itself doesn't use the second processor, but it's available for third party software. OS X does take advantage of multiple CPUs.

I know this is quite the old thread, but I was under the impression that the G4 Macs that can boot OS 9 are quite limited. That is, not every G4 Mac will boot OS 9. For example, the G4 Mac Mini. That's OSX only. The iMacs were that way as well, the cutoff being 800MHz and below models only. Is this correct?